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Bryndal I, Stolarczyk M, Mikołajczyk A, Krupińska M, Pyra A, Mączyński M, Matera-Witkiewicz A. Pyrimidine Schiff Bases: Synthesis, Structural Characterization and Recent Studies on Biological Activities. Int J Mol Sci 2024; 25:2076. [PMID: 38396753 PMCID: PMC10889512 DOI: 10.3390/ijms25042076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Recently, 5-[(4-ethoxyphenyl)imino]methyl-N-(4-fluorophenyl)-6-methyl-2-phenylpyrimidin-4-amine has been synthesized, characterized, and evaluated for its antibacterial activity against Enterococcus faecalis in combination with antineoplastic activity against gastric adenocarcinoma. In this study, new 5-iminomethylpyrimidine compounds were synthesized which differ in the substituent(s) of the aromatic ring attached to the imine group. The structures of newly obtained pyrimidine Schiff bases were established by spectroscopy techniques (ESI-MS, FTIR and 1H NMR). To extend the current knowledge about the features responsible for the biological activity of the new 5-iminomethylpyrimidine derivatives, low-temperature single-crystal X-ray analyses were carried out. For all studied crystals, intramolecular N-H∙∙∙N hydrogen bonds and intermolecular C-H∙∙∙F interactions were observed and seemed to play an essential role in the formation of the structures. Simultaneously, their biological properties based on their cytotoxic features were compared with the activities of the Schiff base (III) published previously. Moreover, computational investigations, such as ADME prediction analysis and molecular docking, were also performed on the most active new Schiff base (compound 4b). These results were compared with the highest active compound III.
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Affiliation(s)
- Iwona Bryndal
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (M.S.); (M.M.)
| | - Marcin Stolarczyk
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (M.S.); (M.M.)
| | - Aleksandra Mikołajczyk
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (A.M.); (M.K.); (A.M.-W.)
| | - Magdalena Krupińska
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (A.M.); (M.K.); (A.M.-W.)
| | - Anna Pyra
- Faculty of Chemistry, University of Wroclaw, 14 Joliot-Curie, 50-383 Wrocław, Poland;
| | - Marcin Mączyński
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (M.S.); (M.M.)
| | - Agnieszka Matera-Witkiewicz
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wrocław, Poland; (A.M.); (M.K.); (A.M.-W.)
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Stolarczyk M, Matera-Witkiewicz A, Wolska A, Krupińska M, Mikołajczyk A, Pyra A, Bryndal I. Synthesis, Crystal Structure, and Biological Evaluation of Novel 5-Hydroxymethylpyrimidines. MATERIALS (BASEL, SWITZERLAND) 2021; 14:6916. [PMID: 34832318 PMCID: PMC8618934 DOI: 10.3390/ma14226916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 12/02/2022]
Abstract
Pyrimidine displays a wide array of bioactivities, and thence, it is still considered a potent unit of new drug research. Its derivative, 5-hydroxymethylpyrimidine, can be found as a scaffold of nontypical nitrogen bases in DNA and as a core of some natural bioactive compounds. In this study, we obtained a series of 5-hydroxymethylpyrimidines that vary in the 4-position by the reduction of proper esters. All compounds were characterized by spectroscopic analysis, and single-crystal X-ray diffraction was performed for some of them. Biological investigations estimated cytotoxic properties against normal (RPTEC) and cancer (HeLa, HepaRG, Caco-2, AGS, A172) cell lines. It was found that the derivatives with an aliphatic amino group at the 4-position are generally less toxic to normal cells than those with a benzylsulfanyl group. Moreover, compounds with bulky constituents exhibit better anticancer properties, though at a moderate level. The specific compounds were chosen due to their most promising IC50 concentration for in silico study. Furthermore, antimicrobial activity tests were performed against six strains of bacteria and one fungus. They demonstrated that only derivatives with at least three carbon chain amino groups at the 4-position have weak antibacterial properties, and only the derivative with 4-benzylsulfanyl constituent exhibits any antifungal action.
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Affiliation(s)
- Marcin Stolarczyk
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wroclaw, Poland; (M.S.); (I.B.)
| | - Agnieszka Matera-Witkiewicz
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wroclaw, Poland; (A.W.); (M.K.); (A.M.)
| | - Aleksandra Wolska
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wroclaw, Poland; (A.W.); (M.K.); (A.M.)
| | - Magdalena Krupińska
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wroclaw, Poland; (A.W.); (M.K.); (A.M.)
| | - Aleksandra Mikołajczyk
- Screening Biological Activity Assays and Collection of Biological Material Laboratory, Wroclaw Medical University, 211A Borowska, 50-556 Wroclaw, Poland; (A.W.); (M.K.); (A.M.)
| | - Anna Pyra
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie Street 14, 50-383 Wroclaw, Poland;
| | - Iwona Bryndal
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 211A Borowska, 50-556 Wroclaw, Poland; (M.S.); (I.B.)
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Al-Waleedy SAH, Mohamed SK, Mague JT, Akkurt M, Abbady MS, Bakhite EA. Crystal structure and Hirshfeld surface analysis of ethyl 2-({5-acetyl-3-cyano-6-methyl-4-[( E)-2-phenyl-ethen-yl]pyridin-2-yl}sulfan-yl)acetate. Acta Crystallogr E Crystallogr Commun 2021; 77:730-733. [PMID: 34513020 PMCID: PMC8382064 DOI: 10.1107/s2056989021005600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
In the title mol-ecule, C21H20N2O3S, the styryl and ester substituents are displaced to opposite sides of the plane of the pyridine ring. In the crystal, C-H⋯O hydrogen bonds form chains extending parallel to the a-axis direction, which pack with partial inter-calation of the styryl and ester substituents. A Hirshfeld surface analysis indicates that the most significant contributions to the crystal packing are from H⋯H (43.6%), C⋯H/H⋯C (15.6%), O⋯H/H⋯O (14.9%) and N⋯H/H⋯N (11.2%) contacts.
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Affiliation(s)
| | - Shaaban K. Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, M1 5GD, England
- Chemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey
| | - Mohamed S. Abbady
- Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Etify A. Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
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Naves LFN, Borges NM, Custodio JMF, Vaz WF, Bastos RM, Cunha S, Napolitano HB. Structural insights into the biological activity of a thioxopyrimidine derivative. J Mol Model 2021; 27:73. [PMID: 33547505 DOI: 10.1007/s00894-021-04700-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/27/2021] [Indexed: 11/28/2022]
Abstract
Bacterial resistance to the main widespread antibiotics, such as those based on quinolones, is a concern of the scientific community, leading to the search for new classes of molecules that can be used as an alternative. Here, we investigate the crystalline and chemical characteristics of a thioxopyrimide to understand its demonstrated biological activity and to identify which portion of the molecule can be used as a framework to develop new antibiotics. For this purpose, structural studies of ethyl 4-methyl-2-phenyl-6-thioxo-1,6-dihydro-5-pyrimidinecarboxylate were carried out aided by Hirshfeld surface analysis, as well as theoretical calculations on frontier molecular orbitals, molecular electrostatic potential, and conformational stability, in addition to docking studies targeting topoisomerase IV. The docking results show a reasonable accommodation of the molecule at the topoisomerase IV binding site and interact mainly by hydrogen bonds between the thioxopyrimidine portion with Glu198, Thr292, and Gly225, aided by hydrophobic interactions involving the rest of the molecule. These results suggest a relationship between the antibacterial activity shown mainly with the 4-thioxopyrimidine portion, leading to the investigation of new compounds that use this scaffold.
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Affiliation(s)
- Luiz F N Naves
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
| | - Nadia M Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
| | - Jean M F Custodio
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil. .,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46665, USA.
| | - Wesley F Vaz
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
| | - Rodrigo M Bastos
- Instituto de Química, Universidade Federal da Bahia, Campus de Ondina, Salvador, BA, 40170-115, Brazil
| | - Silvio Cunha
- Instituto de Química, Universidade Federal da Bahia, Campus de Ondina, Salvador, BA, 40170-115, Brazil
| | - Hamilton B Napolitano
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
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Ali A, Khalid M, Rehman MA, Anwar F, Zain-Ul-Aabidin H, Akhtar MN, Khan MU, Braga AA, Assiri MA, Imran M. An Experimental and Computational Exploration on the Electronic, Spectroscopic, and Reactivity Properties of Novel Halo-Functionalized Hydrazones. ACS OMEGA 2020; 5:18907-18918. [PMID: 32775892 PMCID: PMC7408231 DOI: 10.1021/acsomega.0c02128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/29/2020] [Indexed: 05/18/2023]
Abstract
Herein, halo-functionalized hydrazone derivatives "2-[(6'-chloroazin-2'-yl)oxy]-N'-(2-fluorobenzylidene) aceto-hydrazone (CPFH), 2-[(6'-chloroazin-2'-yl)oxy]-N'-(2-chlorobenzylidene) aceto-hydrazones (CCPH), 2-[(6'-chloroazin-2'-yl)oxy]-N'-(2-bromobenzylidene) aceto-hydrazones (BCPH)" were synthesized and structurally characterized using FTIR, 1H-NMR, 13C-NMR, and UV-vis spectroscopic techniques. Computational studies using density functional theory (DFT) and time dependent DFT at CAM-B3LYP/6-311G (d,p) level of theory were performed for comparison with spectroscopic data (FT-IR, UV-vis) and for elucidation of the structural parameters, natural bond orbitals (NBOs), natural population analysis, frontier molecular orbital (FMO) analysis and nonlinear optical (NLO) properties of hydrazones derivatives (CPFH, CCPH, and BCPH). Consequently, an excellent complement between the experimental data and the DFT-based results was achieved. The NBO analysis confirmed that the presence of hyper conjugative interactions was pivotal cause for stability of the investigated compounds. The energy gaps in CPFH, CCPH, and BCPH were found as 7.278, 7.241, and 7.229 eV, respectively. Furthermore, global reactivity descriptors were calculated using the FMO energies in which global hardness revealed that CPFH was more stable and less reactive as compared to BCPH and CCPH. NLO findings disclosed that CPFH, CCPH, and BCPH have superior properties as compared to the prototype standard compound, which unveiled their potential applications for optoelectronic technology.
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Affiliation(s)
- Akbar Ali
- Department
of Chemistry, University of Sargodha, Sargodha 40100, Pakistan
| | - Muhammad Khalid
- Department
of Chemistry, Khwaja Fareed University of
Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | | | - Farooq Anwar
- Department
of Chemistry, University of Sargodha, Sargodha 40100, Pakistan
| | | | - Muhammad Nadeem Akhtar
- Department
of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | | | | | - Mohammed A. Assiri
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Muhammad Imran
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
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Akram M, Adeel M, Khalid M, Tahir MN, Aliabad HAR, Ullah MA, Iqbal J, Braga AA. Highly efficient one pot palladium-catalyzed synthesis of 3,5-bis (arylated) pyridines: Comparative experimental and DFT studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hussain A, Khan MU, Ibrahim M, Khalid M, Ali A, Hussain S, Saleem M, Ahmad N, Muhammad S, Al-Sehemi AG, Sultan A. Structural parameters, electronic, linear and nonlinear optical exploration of thiopyrimidine derivatives: A comparison between DFT/TDDFT and experimental study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127183] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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